StatAlign statistics

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StatAlign specifications


Unique identifier OMICS_03743
Name StatAlign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Adam Novak <>

Publications for StatAlign

StatAlign in publications

PMCID: 5850488
PMID: 28453724
DOI: 10.1093/molbev/msx137

[…] nevertheless, a single maximum a posteriori (map) pairwise alignment may be obtained from the alignment samples and used for downstream analysis., etdbn and several other alignment methods (namely statalign, bali-phy, muscle, and mafft) were used to infer pairwise alignments from simulated and real data under various combinations of data observations, for example: an amino acid sequence pair […]

PMCID: 5123300
DOI: 10.1186/s12864-016-3101-8

[…] the parameters of the divide-and-conquer strategy (especially the maximum subset size) can be adjusted to suit the given base msa method, this extension can be easily done. thus, methods such as statalign [], which may be limited to even smaller datasets, could also be tested in this framework. similarly, methods such as pagan [] are impacted by dataset size and the challenge in estimating […]

PMCID: 4527676
PMID: 26247465
DOI: 10.1371/journal.pone.0129668

[…] and the cyclostome hbs (lamprey, hagfish) ()., analyses using the bayesian model for the joint evolution of sequence and structure were carried out using the structalign plugin [, ], as part of the statalign package []. four independent mcmc chains were run, starting from different initial configurations. the smaller dataset was run for a burn-in period of 1m iterations, followed by a sampling […]

PMCID: 3667108
PMID: 23634662
DOI: 10.1186/1471-2105-14-149

[…] homoplasy and alignment uncertainty with high accuracy or can be used to decrease alignment uncertainty effects in downstream analyses, for instance protein secondary structure prediction []., statalign is a statistical alignment software package [] that allows joint bayesian analysis of multiple alignments, phylogenetic trees and evolutionary parameters. the background model […]

PMCID: 2666655
PMID: 19321000
DOI: 10.1186/1743-422X-6-36

[…] bootstrapped maximum likelihood phylogenetic trees using phyml. as there is a large degree of uncertainty associated with aligning such divergent amino acid sequences, we also used the program statalign to directly construct phylogenetic trees in which alignment uncertainty is explicitly accounted for. we then used the absolute consensus of the phyml and statalign trees, collapsing […]

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StatAlign institution(s)
Department of Computer Science, University of North Carolina at Chapel Hill, NC, USA; Department of Mathematics, Reykjavik University, Reykjavik, Iceland; Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa; Department of Statistics, University of Oxford, Oxford, UK; Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
StatAlign funding source(s)
Funding was provided by the EU COGANGS Grant, BBSRC (AN), and EPSRC (JWJA).

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